Starting phenix.real_space_refine on Sun Jun 15 06:03:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w53_32313/06_2025/7w53_32313.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w53_32313/06_2025/7w53_32313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w53_32313/06_2025/7w53_32313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w53_32313/06_2025/7w53_32313.map" model { file = "/net/cci-nas-00/data/ceres_data/7w53_32313/06_2025/7w53_32313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w53_32313/06_2025/7w53_32313.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 62 5.16 5 C 5521 2.51 5 N 1524 2.21 5 O 1603 1.98 5 H 8644 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17354 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3443 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 3 Chain: "B" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5109 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 136 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3504 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 4277 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 3 Time building chain proxies: 8.43, per 1000 atoms: 0.49 Number of scatterers: 17354 At special positions: 0 Unit cell: (117.72, 133.92, 102.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 O 1603 8.00 N 1524 7.00 C 5521 6.00 H 8644 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 219 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.7% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.968A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.952A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 218 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.232A pdb=" N THR A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.572A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 4.089A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.682A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 60 through 86 Processing helix chain 'R' and resid 87 through 90 Processing helix chain 'R' and resid 95 through 112 removed outlier: 4.117A pdb=" N LEU R 99 " --> pdb=" O THR R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 120 Processing helix chain 'R' and resid 131 through 165 Processing helix chain 'R' and resid 165 through 173 Processing helix chain 'R' and resid 174 through 198 removed outlier: 4.104A pdb=" N ARG R 180 " --> pdb=" O ALA R 176 " (cutoff:3.500A) Proline residue: R 195 - end of helix Processing helix chain 'R' and resid 227 through 263 removed outlier: 3.641A pdb=" N VAL R 231 " --> pdb=" O LEU R 227 " (cutoff:3.500A) Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 290 through 323 Proline residue: R 312 - end of helix removed outlier: 3.704A pdb=" N ARG R 317 " --> pdb=" O PHE R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 357 Proline residue: R 353 - end of helix Processing helix chain 'R' and resid 360 through 365 removed outlier: 4.162A pdb=" N GLU R 365 " --> pdb=" O SER R 361 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.236A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.519A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B 322 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.512A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.312A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 158 removed outlier: 3.524A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLN B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 162 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.506A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.767A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.701A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.875A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.875A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.281A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 200 through 202 453 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.50 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8613 1.02 - 1.22: 45 1.22 - 1.42: 3769 1.42 - 1.63: 5010 1.63 - 1.83: 93 Bond restraints: 17530 Sorted by residual: bond pdb=" SG CYS R 219 " pdb=" HG CYS R 219 " ideal model delta sigma weight residual 1.200 1.344 -0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" SG CYS R 134 " pdb=" HG CYS R 134 " ideal model delta sigma weight residual 1.200 1.343 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" SG CYS R 241 " pdb=" HG CYS R 241 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" SG CYS B 299 " pdb=" HG CYS B 299 " ideal model delta sigma weight residual 1.200 1.338 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" ND2 ASN A 216 " pdb="HD22 ASN A 216 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 ... (remaining 17525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.24: 31493 6.24 - 12.48: 15 12.48 - 18.72: 2 18.72 - 24.96: 0 24.96 - 31.21: 2 Bond angle restraints: 31512 Sorted by residual: angle pdb=" N PRO E 236 " pdb=" CA PRO E 236 " pdb=" C PRO E 236 " ideal model delta sigma weight residual 112.36 81.15 31.21 2.06e+00 2.36e-01 2.29e+02 angle pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" C TYR E 235 " ideal model delta sigma weight residual 108.66 135.51 -26.85 2.16e+00 2.14e-01 1.55e+02 angle pdb=" N ASP B 296 " pdb=" CA ASP B 296 " pdb=" C ASP B 296 " ideal model delta sigma weight residual 110.50 96.45 14.05 1.41e+00 5.03e-01 9.93e+01 angle pdb=" N PHE B 240 " pdb=" CA PHE B 240 " pdb=" C PHE B 240 " ideal model delta sigma weight residual 110.08 102.09 7.99 1.38e+00 5.25e-01 3.36e+01 angle pdb=" N ILE A 184 " pdb=" CA ILE A 184 " pdb=" C ILE A 184 " ideal model delta sigma weight residual 109.34 121.29 -11.95 2.08e+00 2.31e-01 3.30e+01 ... (remaining 31507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7517 17.86 - 35.72: 495 35.72 - 53.58: 180 53.58 - 71.44: 61 71.44 - 89.31: 9 Dihedral angle restraints: 8262 sinusoidal: 4452 harmonic: 3810 Sorted by residual: dihedral pdb=" C TYR E 235 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " ideal model delta harmonic sigma weight residual -122.60 -137.26 14.66 0 2.50e+00 1.60e-01 3.44e+01 dihedral pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " ideal model delta harmonic sigma weight residual 122.80 137.08 -14.28 0 2.50e+00 1.60e-01 3.26e+01 dihedral pdb=" N PRO E 236 " pdb=" C PRO E 236 " pdb=" CA PRO E 236 " pdb=" CB PRO E 236 " ideal model delta harmonic sigma weight residual 115.10 102.07 13.03 0 2.50e+00 1.60e-01 2.72e+01 ... (remaining 8259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 1355 0.202 - 0.404: 4 0.404 - 0.605: 0 0.605 - 0.807: 0 0.807 - 1.009: 1 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.54e+01 chirality pdb=" CA PRO E 236 " pdb=" N PRO E 236 " pdb=" C PRO E 236 " pdb=" CB PRO E 236 " both_signs ideal model delta sigma weight residual False 2.72 2.95 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1357 not shown) Planarity restraints: 2589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 216 " -0.308 2.00e-02 2.50e+03 3.57e-01 1.91e+03 pdb=" CG ASN A 216 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 216 " 0.300 2.00e-02 2.50e+03 pdb=" ND2 ASN A 216 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 216 " 0.529 2.00e-02 2.50e+03 pdb="HD22 ASN A 216 " -0.547 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 259 " -0.250 2.00e-02 2.50e+03 2.64e-01 1.05e+03 pdb=" CG ASN A 259 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN A 259 " 0.245 2.00e-02 2.50e+03 pdb=" ND2 ASN A 259 " -0.005 2.00e-02 2.50e+03 pdb="HD21 ASN A 259 " 0.388 2.00e-02 2.50e+03 pdb="HD22 ASN A 259 " -0.382 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 298 " 0.139 2.00e-02 2.50e+03 1.38e-01 2.86e+02 pdb=" CG ASN B 298 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN B 298 " -0.133 2.00e-02 2.50e+03 pdb=" ND2 ASN B 298 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 298 " -0.195 2.00e-02 2.50e+03 pdb="HD22 ASN B 298 " 0.198 2.00e-02 2.50e+03 ... (remaining 2586 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 316 2.05 - 2.69: 27725 2.69 - 3.33: 52097 3.33 - 3.96: 66630 3.96 - 4.60: 105385 Nonbonded interactions: 252153 Sorted by model distance: nonbonded pdb=" O ILE B 63 " pdb=" HG SER B 321 " model vdw 1.415 2.450 nonbonded pdb=" OE2 GLU E 5 " pdb=" H CYS E 95 " model vdw 1.462 2.450 nonbonded pdb="HH12 ARG A 15 " pdb=" O VAL B 95 " model vdw 1.478 2.450 nonbonded pdb=" OD1 ASN C 9 " pdb="HD22 ASN R 196 " model vdw 1.487 2.450 nonbonded pdb=" O ASP B 71 " pdb=" H ARG B 73 " model vdw 1.510 2.450 ... (remaining 252148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.290 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.590 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 8887 Z= 0.334 Angle : 0.861 31.205 12031 Z= 0.503 Chirality : 0.055 1.009 1360 Planarity : 0.004 0.051 1528 Dihedral : 12.622 89.306 3210 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.63 % Allowed : 6.33 % Favored : 93.04 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1082 helix: 0.03 (0.24), residues: 377 sheet: -0.54 (0.30), residues: 272 loop : -0.60 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 310 HIS 0.006 0.002 HIS B 96 PHE 0.015 0.002 PHE B 240 TYR 0.027 0.002 TYR E 235 ARG 0.005 0.001 ARG R 292 Details of bonding type rmsd hydrogen bonds : bond 0.17727 ( 449) hydrogen bonds : angle 7.29365 ( 1266) SS BOND : bond 0.00812 ( 1) SS BOND : angle 1.91119 ( 2) covalent geometry : bond 0.00687 ( 8886) covalent geometry : angle 0.86023 (12029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 226 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7150 (mt0) REVERT: A 319 SER cc_start: 0.5546 (t) cc_final: 0.5312 (m) REVERT: B 228 THR cc_start: 0.7805 (p) cc_final: 0.7432 (t) REVERT: R 158 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6783 (mm-30) REVERT: R 293 ARG cc_start: 0.6913 (ptt-90) cc_final: 0.6388 (ptm160) outliers start: 6 outliers final: 3 residues processed: 230 average time/residue: 0.6951 time to fit residues: 199.6567 Evaluate side-chains 175 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain R residue 240 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 216 ASN ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.158674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123322 restraints weight = 33660.919| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.20 r_work: 0.3384 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8887 Z= 0.127 Angle : 0.568 7.205 12031 Z= 0.307 Chirality : 0.041 0.147 1360 Planarity : 0.005 0.104 1528 Dihedral : 6.018 56.469 1216 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.74 % Allowed : 10.34 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1082 helix: 1.26 (0.25), residues: 385 sheet: -0.47 (0.31), residues: 256 loop : -0.61 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 87 HIS 0.006 0.001 HIS A 324 PHE 0.010 0.001 PHE R 334 TYR 0.015 0.001 TYR R 135 ARG 0.006 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 449) hydrogen bonds : angle 5.32648 ( 1266) SS BOND : bond 0.00322 ( 1) SS BOND : angle 1.47766 ( 2) covalent geometry : bond 0.00260 ( 8886) covalent geometry : angle 0.56755 (12029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7365 (mt0) REVERT: A 319 SER cc_start: 0.5797 (t) cc_final: 0.5482 (m) REVERT: B 263 ASP cc_start: 0.7524 (t0) cc_final: 0.7011 (t0) REVERT: E 171 ASN cc_start: 0.8282 (p0) cc_final: 0.8081 (p0) REVERT: G 11 GLN cc_start: 0.7812 (tm-30) cc_final: 0.7284 (tt0) REVERT: G 22 GLU cc_start: 0.6804 (tp30) cc_final: 0.6478 (tp30) REVERT: R 143 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6682 (ttp) REVERT: R 158 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7378 (mm-30) REVERT: R 223 ARG cc_start: 0.7761 (mmt-90) cc_final: 0.7128 (mmm160) REVERT: R 293 ARG cc_start: 0.6798 (ptt-90) cc_final: 0.6132 (ptm160) REVERT: R 325 GLN cc_start: 0.7673 (pp30) cc_final: 0.7156 (pp30) outliers start: 7 outliers final: 4 residues processed: 200 average time/residue: 0.5615 time to fit residues: 146.4866 Evaluate side-chains 178 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 173 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 143 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 30 optimal weight: 0.0870 chunk 56 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 115 ASN B 300 ASN ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.157374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122006 restraints weight = 33860.671| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.19 r_work: 0.3369 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8887 Z= 0.145 Angle : 0.543 7.260 12031 Z= 0.293 Chirality : 0.040 0.143 1360 Planarity : 0.004 0.068 1528 Dihedral : 5.575 58.456 1214 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.16 % Allowed : 11.18 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1082 helix: 1.67 (0.26), residues: 385 sheet: -0.61 (0.31), residues: 258 loop : -0.51 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 87 HIS 0.008 0.001 HIS R 331 PHE 0.011 0.001 PHE R 334 TYR 0.020 0.001 TYR R 135 ARG 0.003 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 449) hydrogen bonds : angle 4.95568 ( 1266) SS BOND : bond 0.00786 ( 1) SS BOND : angle 1.56392 ( 2) covalent geometry : bond 0.00308 ( 8886) covalent geometry : angle 0.54306 (12029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7427 (mt0) REVERT: A 319 SER cc_start: 0.5830 (t) cc_final: 0.5510 (m) REVERT: B 21 ASN cc_start: 0.7685 (m-40) cc_final: 0.7044 (m-40) REVERT: B 263 ASP cc_start: 0.7565 (t0) cc_final: 0.7353 (t0) REVERT: E 41 GLU cc_start: 0.7375 (tp30) cc_final: 0.7122 (tp30) REVERT: E 171 ASN cc_start: 0.8329 (p0) cc_final: 0.8117 (p0) REVERT: G 11 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7146 (tt0) REVERT: R 98 TYR cc_start: 0.8653 (m-80) cc_final: 0.8394 (m-80) REVERT: R 143 MET cc_start: 0.6921 (ttt) cc_final: 0.6575 (ttm) REVERT: R 158 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7246 (mm-30) REVERT: R 190 MET cc_start: 0.6357 (tpp) cc_final: 0.5983 (tpp) REVERT: R 223 ARG cc_start: 0.7725 (mmt-90) cc_final: 0.7147 (mmm160) REVERT: R 228 TYR cc_start: 0.6809 (OUTLIER) cc_final: 0.6197 (m-80) REVERT: R 293 ARG cc_start: 0.6724 (ptt-90) cc_final: 0.6034 (ptm160) outliers start: 11 outliers final: 7 residues processed: 185 average time/residue: 0.7096 time to fit residues: 173.7618 Evaluate side-chains 176 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 240 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.155587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119959 restraints weight = 33830.163| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.18 r_work: 0.3345 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8887 Z= 0.185 Angle : 0.565 7.507 12031 Z= 0.304 Chirality : 0.041 0.134 1360 Planarity : 0.004 0.060 1528 Dihedral : 5.612 59.276 1213 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.48 % Allowed : 11.50 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1082 helix: 1.73 (0.26), residues: 385 sheet: -0.71 (0.31), residues: 258 loop : -0.57 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 87 HIS 0.009 0.001 HIS R 331 PHE 0.013 0.001 PHE B 204 TYR 0.022 0.002 TYR R 135 ARG 0.007 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 449) hydrogen bonds : angle 4.92554 ( 1266) SS BOND : bond 0.00650 ( 1) SS BOND : angle 1.54571 ( 2) covalent geometry : bond 0.00404 ( 8886) covalent geometry : angle 0.56439 (12029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7673 (mt0) REVERT: A 247 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7491 (ttp80) REVERT: B 24 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7339 (ttp80) REVERT: B 202 ARG cc_start: 0.7559 (mtp-110) cc_final: 0.7158 (mtm110) REVERT: B 239 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.8672 (t80) REVERT: E 41 GLU cc_start: 0.7447 (tp30) cc_final: 0.7106 (tp30) REVERT: R 61 MET cc_start: 0.5590 (tpt) cc_final: 0.5130 (tpp) REVERT: R 64 CYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6727 (p) REVERT: R 143 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6554 (ttm) REVERT: R 190 MET cc_start: 0.6310 (tpp) cc_final: 0.5911 (tpp) REVERT: R 223 ARG cc_start: 0.7725 (mmt-90) cc_final: 0.7124 (mmm160) REVERT: R 293 ARG cc_start: 0.6580 (ptt-90) cc_final: 0.5862 (ptm160) REVERT: R 325 GLN cc_start: 0.7538 (pp30) cc_final: 0.7114 (pp30) outliers start: 14 outliers final: 7 residues processed: 172 average time/residue: 0.6423 time to fit residues: 143.0519 Evaluate side-chains 171 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 240 PHE Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.156333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121187 restraints weight = 34107.733| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.18 r_work: 0.3359 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8887 Z= 0.145 Angle : 0.527 6.826 12031 Z= 0.282 Chirality : 0.040 0.134 1360 Planarity : 0.004 0.054 1528 Dihedral : 5.427 59.894 1213 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.27 % Allowed : 12.13 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1082 helix: 1.95 (0.26), residues: 385 sheet: -0.73 (0.31), residues: 262 loop : -0.51 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 87 HIS 0.006 0.001 HIS R 331 PHE 0.009 0.001 PHE B 204 TYR 0.024 0.001 TYR R 135 ARG 0.008 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 449) hydrogen bonds : angle 4.75788 ( 1266) SS BOND : bond 0.00554 ( 1) SS BOND : angle 1.53381 ( 2) covalent geometry : bond 0.00311 ( 8886) covalent geometry : angle 0.52633 (12029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7445 (mt0) REVERT: B 202 ARG cc_start: 0.7570 (mtp-110) cc_final: 0.7153 (mtm110) REVERT: B 239 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.8755 (t80) REVERT: B 263 ASP cc_start: 0.7556 (t0) cc_final: 0.7271 (t0) REVERT: E 41 GLU cc_start: 0.7510 (tp30) cc_final: 0.7140 (tp30) REVERT: G 11 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7389 (tt0) REVERT: R 61 MET cc_start: 0.5505 (tpt) cc_final: 0.5009 (tpp) REVERT: R 64 CYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6692 (p) REVERT: R 143 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6361 (ttm) REVERT: R 190 MET cc_start: 0.6236 (tpp) cc_final: 0.5691 (tpp) REVERT: R 223 ARG cc_start: 0.7754 (mmt-90) cc_final: 0.7142 (mmm160) REVERT: R 293 ARG cc_start: 0.6671 (ptt-90) cc_final: 0.5875 (ptm160) REVERT: R 294 GLN cc_start: 0.7439 (tm-30) cc_final: 0.7156 (tm-30) REVERT: R 325 GLN cc_start: 0.7536 (pp30) cc_final: 0.7159 (pp30) outliers start: 12 outliers final: 6 residues processed: 175 average time/residue: 0.7713 time to fit residues: 175.7657 Evaluate side-chains 168 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.153977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118914 restraints weight = 34383.729| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.14 r_work: 0.3305 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8887 Z= 0.234 Angle : 0.589 7.858 12031 Z= 0.319 Chirality : 0.041 0.149 1360 Planarity : 0.005 0.054 1528 Dihedral : 5.650 57.303 1213 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.00 % Allowed : 13.19 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1082 helix: 1.82 (0.26), residues: 379 sheet: -0.85 (0.32), residues: 256 loop : -0.65 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 87 HIS 0.008 0.001 HIS R 331 PHE 0.014 0.002 PHE B 204 TYR 0.023 0.002 TYR E 235 ARG 0.008 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 449) hydrogen bonds : angle 4.96134 ( 1266) SS BOND : bond 0.00680 ( 1) SS BOND : angle 1.58551 ( 2) covalent geometry : bond 0.00517 ( 8886) covalent geometry : angle 0.58862 (12029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 3.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7620 (mt0) REVERT: B 128 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8415 (mp) REVERT: B 202 ARG cc_start: 0.7603 (mtp-110) cc_final: 0.7241 (mtm110) REVERT: B 239 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.8958 (t80) REVERT: E 41 GLU cc_start: 0.7450 (tp30) cc_final: 0.7062 (tp30) REVERT: E 54 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8564 (p) REVERT: E 234 GLU cc_start: 0.7407 (tt0) cc_final: 0.7168 (tt0) REVERT: G 11 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7238 (tt0) REVERT: R 143 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6434 (ttm) REVERT: R 190 MET cc_start: 0.6314 (tpp) cc_final: 0.5760 (tpp) REVERT: R 223 ARG cc_start: 0.7750 (mmt-90) cc_final: 0.7146 (mmm160) REVERT: R 293 ARG cc_start: 0.6705 (ptt-90) cc_final: 0.5754 (ptm-80) REVERT: R 325 GLN cc_start: 0.7529 (pp30) cc_final: 0.7156 (pp30) outliers start: 19 outliers final: 12 residues processed: 173 average time/residue: 0.7546 time to fit residues: 173.4674 Evaluate side-chains 170 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 240 PHE Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.155206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120634 restraints weight = 34364.867| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.10 r_work: 0.3330 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8887 Z= 0.203 Angle : 0.570 7.169 12031 Z= 0.305 Chirality : 0.040 0.134 1360 Planarity : 0.004 0.059 1528 Dihedral : 5.570 56.618 1213 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.58 % Allowed : 14.03 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1082 helix: 1.91 (0.26), residues: 379 sheet: -0.89 (0.32), residues: 254 loop : -0.69 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 310 HIS 0.005 0.001 HIS R 331 PHE 0.012 0.002 PHE B 204 TYR 0.018 0.002 TYR E 190 ARG 0.009 0.001 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 449) hydrogen bonds : angle 4.90544 ( 1266) SS BOND : bond 0.00531 ( 1) SS BOND : angle 1.43910 ( 2) covalent geometry : bond 0.00445 ( 8886) covalent geometry : angle 0.56976 (12029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8883 (mttt) cc_final: 0.8229 (mmtt) REVERT: A 24 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7549 (mt0) REVERT: B 128 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8408 (mp) REVERT: B 202 ARG cc_start: 0.7693 (mtp-110) cc_final: 0.7296 (mtm110) REVERT: B 239 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.8883 (t80) REVERT: E 41 GLU cc_start: 0.7517 (tp30) cc_final: 0.7105 (tp30) REVERT: E 234 GLU cc_start: 0.7219 (tt0) cc_final: 0.6942 (tt0) REVERT: G 11 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7223 (tt0) REVERT: R 61 MET cc_start: 0.5458 (tpp) cc_final: 0.5172 (tpp) REVERT: R 64 CYS cc_start: 0.7199 (t) cc_final: 0.6806 (p) REVERT: R 143 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6489 (ttm) REVERT: R 190 MET cc_start: 0.6370 (tpp) cc_final: 0.5906 (tpp) REVERT: R 223 ARG cc_start: 0.7654 (mmt-90) cc_final: 0.7142 (mmm160) REVERT: R 293 ARG cc_start: 0.6776 (ptt-90) cc_final: 0.5999 (ptm160) REVERT: R 294 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7230 (tm-30) REVERT: R 325 GLN cc_start: 0.7523 (pp30) cc_final: 0.7182 (pp30) outliers start: 15 outliers final: 11 residues processed: 170 average time/residue: 0.6141 time to fit residues: 134.3277 Evaluate side-chains 171 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.154774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.119565 restraints weight = 34122.422| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.16 r_work: 0.3332 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8887 Z= 0.186 Angle : 0.555 7.054 12031 Z= 0.298 Chirality : 0.040 0.135 1360 Planarity : 0.004 0.064 1528 Dihedral : 5.490 55.877 1213 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.00 % Allowed : 13.82 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1082 helix: 1.98 (0.26), residues: 379 sheet: -0.94 (0.31), residues: 263 loop : -0.66 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 87 HIS 0.007 0.001 HIS R 331 PHE 0.012 0.001 PHE A 189 TYR 0.018 0.002 TYR E 190 ARG 0.009 0.001 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 449) hydrogen bonds : angle 4.82431 ( 1266) SS BOND : bond 0.00484 ( 1) SS BOND : angle 1.43375 ( 2) covalent geometry : bond 0.00406 ( 8886) covalent geometry : angle 0.55511 (12029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8866 (mttt) cc_final: 0.8177 (mmtt) REVERT: A 24 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7527 (mt0) REVERT: A 300 ARG cc_start: 0.7535 (mtm180) cc_final: 0.7137 (mtm110) REVERT: B 202 ARG cc_start: 0.7695 (mtp-110) cc_final: 0.7250 (mtm110) REVERT: B 239 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.8851 (t80) REVERT: E 41 GLU cc_start: 0.7454 (tp30) cc_final: 0.7040 (tp30) REVERT: E 234 GLU cc_start: 0.7282 (tt0) cc_final: 0.6982 (tt0) REVERT: G 11 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7273 (tt0) REVERT: R 61 MET cc_start: 0.5277 (tpp) cc_final: 0.4981 (tpp) REVERT: R 64 CYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6754 (p) REVERT: R 143 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6397 (ttm) REVERT: R 190 MET cc_start: 0.6209 (tpp) cc_final: 0.5764 (tpp) REVERT: R 223 ARG cc_start: 0.7686 (mmt-90) cc_final: 0.7104 (mmm160) REVERT: R 293 ARG cc_start: 0.6841 (ptt-90) cc_final: 0.5995 (ptm160) REVERT: R 325 GLN cc_start: 0.7568 (pp30) cc_final: 0.7192 (pp30) outliers start: 19 outliers final: 14 residues processed: 171 average time/residue: 0.6162 time to fit residues: 136.0003 Evaluate side-chains 173 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.157219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122242 restraints weight = 34016.691| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.16 r_work: 0.3371 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8887 Z= 0.125 Angle : 0.517 6.229 12031 Z= 0.274 Chirality : 0.039 0.135 1360 Planarity : 0.004 0.064 1528 Dihedral : 5.162 54.973 1213 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.48 % Allowed : 14.35 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1082 helix: 2.29 (0.26), residues: 379 sheet: -0.88 (0.31), residues: 269 loop : -0.54 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 87 HIS 0.008 0.001 HIS R 331 PHE 0.010 0.001 PHE A 189 TYR 0.024 0.001 TYR R 135 ARG 0.011 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 449) hydrogen bonds : angle 4.59807 ( 1266) SS BOND : bond 0.00353 ( 1) SS BOND : angle 1.53732 ( 2) covalent geometry : bond 0.00267 ( 8886) covalent geometry : angle 0.51632 (12029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8742 (mttt) cc_final: 0.8021 (mmtt) REVERT: A 24 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7512 (mt0) REVERT: A 247 ARG cc_start: 0.7506 (ttp80) cc_final: 0.7225 (ttp80) REVERT: A 300 ARG cc_start: 0.7579 (mtm180) cc_final: 0.7155 (mtm110) REVERT: B 202 ARG cc_start: 0.7699 (mtp-110) cc_final: 0.7248 (mtm110) REVERT: B 239 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.8722 (t80) REVERT: E 41 GLU cc_start: 0.7504 (tp30) cc_final: 0.7068 (tp30) REVERT: E 171 ASN cc_start: 0.8361 (p0) cc_final: 0.8139 (p0) REVERT: E 234 GLU cc_start: 0.7062 (tt0) cc_final: 0.6854 (tt0) REVERT: G 11 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7248 (tt0) REVERT: R 143 MET cc_start: 0.6840 (ttt) cc_final: 0.6344 (ttm) REVERT: R 158 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7694 (mm-30) REVERT: R 190 MET cc_start: 0.6219 (tpp) cc_final: 0.5784 (tpp) REVERT: R 223 ARG cc_start: 0.7617 (mmt-90) cc_final: 0.7082 (mmm160) REVERT: R 293 ARG cc_start: 0.6817 (ptt-90) cc_final: 0.5998 (ptm160) REVERT: R 294 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7263 (tm-30) outliers start: 14 outliers final: 10 residues processed: 187 average time/residue: 0.5904 time to fit residues: 143.2776 Evaluate side-chains 182 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.157351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123336 restraints weight = 33985.520| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.10 r_work: 0.3370 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8887 Z= 0.143 Angle : 0.530 6.681 12031 Z= 0.280 Chirality : 0.039 0.134 1360 Planarity : 0.004 0.068 1528 Dihedral : 5.148 54.260 1213 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.27 % Allowed : 14.66 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1082 helix: 2.27 (0.26), residues: 379 sheet: -0.84 (0.31), residues: 269 loop : -0.54 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 87 HIS 0.010 0.001 HIS R 331 PHE 0.010 0.001 PHE R 334 TYR 0.020 0.001 TYR R 135 ARG 0.011 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 449) hydrogen bonds : angle 4.62201 ( 1266) SS BOND : bond 0.00408 ( 1) SS BOND : angle 1.55736 ( 2) covalent geometry : bond 0.00310 ( 8886) covalent geometry : angle 0.52953 (12029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8790 (mttt) cc_final: 0.8138 (mmtt) REVERT: A 24 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7561 (mt0) REVERT: A 247 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7187 (ttp80) REVERT: A 300 ARG cc_start: 0.7578 (mtm180) cc_final: 0.7138 (mtm110) REVERT: B 202 ARG cc_start: 0.7685 (mtp-110) cc_final: 0.7285 (mtm110) REVERT: B 239 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8784 (t80) REVERT: E 41 GLU cc_start: 0.7410 (tp30) cc_final: 0.6979 (tp30) REVERT: E 171 ASN cc_start: 0.8412 (p0) cc_final: 0.8180 (p0) REVERT: G 11 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7213 (tt0) REVERT: R 64 CYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6775 (p) REVERT: R 143 MET cc_start: 0.6868 (ttt) cc_final: 0.6354 (ttm) REVERT: R 158 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7722 (mm-30) REVERT: R 190 MET cc_start: 0.6252 (tpp) cc_final: 0.5847 (tpp) REVERT: R 220 MET cc_start: 0.6025 (ttt) cc_final: 0.5748 (ttp) REVERT: R 223 ARG cc_start: 0.7588 (mmt-90) cc_final: 0.7119 (mmm160) REVERT: R 293 ARG cc_start: 0.6818 (ptt-90) cc_final: 0.6000 (ptm160) REVERT: R 294 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7220 (tm-30) outliers start: 12 outliers final: 9 residues processed: 182 average time/residue: 0.6054 time to fit residues: 142.5356 Evaluate side-chains 182 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 HIS R 335 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.158236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123495 restraints weight = 33983.436| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.17 r_work: 0.3392 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8887 Z= 0.111 Angle : 0.505 6.006 12031 Z= 0.266 Chirality : 0.039 0.134 1360 Planarity : 0.004 0.066 1528 Dihedral : 4.935 53.575 1213 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.95 % Allowed : 14.77 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1082 helix: 2.45 (0.26), residues: 380 sheet: -0.71 (0.31), residues: 269 loop : -0.47 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 87 HIS 0.007 0.001 HIS R 331 PHE 0.009 0.001 PHE A 189 TYR 0.014 0.001 TYR R 135 ARG 0.011 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 449) hydrogen bonds : angle 4.46769 ( 1266) SS BOND : bond 0.00324 ( 1) SS BOND : angle 1.66329 ( 2) covalent geometry : bond 0.00238 ( 8886) covalent geometry : angle 0.50485 (12029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10767.47 seconds wall clock time: 188 minutes 15.98 seconds (11295.98 seconds total)